Improving diagnosis of tuberculosis from urine cell-free DNA

Thesis (Ph.D.)--University of Washington, 2021Tuberculosis (TB) is the leading cause of infectious disease-related mortality worldwide, in part due to limitations in rapid diagnostics. Current TB tests rely on sputum samples, which are difficult to collect from many patients, including people living with HIV, those who are severely ill, and children, and may not detect extrapulmonary TB. Rapid sputum-based tests also have reduced sensitivity in these same patient populations, who more often have paucibacillary TB. There is a critical need for TB diagnostics that target more easily accessible samples, such as urine. Transrenal urine cell-free DNA (cfDNA) is a promising biomarker for TB but is challenging to detect because of the short length (<100 bp) and low concentration of TB-specific fragments. We aimed to increase the sensitivity of TB diagnosis from urine cfDNA by improving recovery of short fragments during the sample preparation step. Here, I present the development of a sequence-specific purification method for cfDNA with